Table 5 Predicted phage like elements using a comparative protein based approach. Phage elements detected in other genomes using orthology to e14 proteins as a criterion. Clustering of orthologous proteins (COG hits) for the e14 proteins in different organisms was examined. Only those organisms with two or more COG hits in the e14 element are listed. Estimates of the boundaries of the phage element are provided. 26 phage related regions could be identified by this analysis out of which 23 are already known phage areas in the bacterial genomes. Two (labeled P2 and P3) of the remaining three regions are probably non-phage areas. *The regions which have not been previously identified as prophage element have been marked as P1, P2 and P3. $Denotes approximate boundaries.
From: Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome
Organism | Proteins in e14 | Related COG member | locus (approx.) | prophage name |
|---|---|---|---|---|
E. coli O157:H7 EDL933 | b1149, b1151, b1159 | z1359, z1362, z1356 | 1250302–1295563 | CP-933M |
|  | b1149, b1151, b1158, b1159 | z1803, z1806, z1817, z1800 | 1626570–1674696 | CP-933N |
|  | b1149, b1149, b1151, b1159 | z6045, z6070, z6042, z6047 | 2271618–2331237 | CP-933P |
|  | b1145, b1154, b1155, b1157, b1158 | z0309, z0314, z0315, z0317, zpinH | 300060–310646 | CP-933H |
|  | b1140, b1141, b1145, b1155, b1157 | z1866, z1867, zumuD, z1920, z1918 | 1701990–1749459 | CP-933X |
|  | b1140, b1143, b1155 | zintT, z2978, z2983 | 2668339–2689384 | CP-933T |
|  | b1149, b1151 | z1854, z1849 | 1678701–1693737 | CP-933C |
|  | b1140, b1145 | zintU, z3126 | 2743223–2788401 | CP-933U |
|  | b1140, b1145 | zintO, z2090 | 1849324–1929903 | CP-933O |
|  | b1145, b1149, b1151 | z3358, z3332, z3328 | 2966157–3015089 | CP-933V |
E. coli K-12 | b1156, b1158 | ybcx, ybck | 564025–585326 | DLP12 |
|  | b1156, b1157, b1158 | ynac, stfr, pinr | 1409966–1433025 | rac |
|  | b1156, b1157, b1158 | ydfm, ydfn, pinq | 1630450–1646830 | qin |
|  | b1154, b1156 | yfdk, tfaS | 2464404–2474619 | KpLE1, CPS-53 |
B. subtilis 168 | b1149, b1158 | BS_lexA, BS_yneB | $1902658–1919056 | *P1 |
|  | b1151, b1152 | BS_ykeA, BS_xkdT | 1316849–1347491 | PBSX |
|  | b1152, b1158 | BS_yqbT, BS_spoIVCA | $2652219–2700977 | SKIN |
M. loti MAFF303099 | b1149, b1151 | Mlr8521, Mlr8522 | $6974260–7021772 | Meso2 |
|  | b1143, b1149 | Mlr4761, Mlr4759 | $3776480–3781495 | *P2 |
C. crescentus | b1150, b1154, b1157 | CC1890, CC1902, CC1904 | $2096699–2098302 | *P3 |
X. fastidiosa 9a5c | b1140, b1149 | XF1642, XF1645 | 1595657–1629967 | XfP4 |
|  | b1140, b1152 | XF1555, XF1598 | 1519081–1532748 | XfP3 |
N. meningitidis Z2491 (serogroup A) | b1152, b1153, b1157 | NMA1323, NMA1324, NMA1325 | 1207176–1236496 | Pnm2 |
| Â | b1152, b1153 | NMA1826, NMA1825 | 1768530 to 1807766 | Pnm1 |
S. pyogenens SF370 (serotype M1) | b1140, b1159 | spy1488, spy1468 | 1189125–1222634 | 370.2 |
|  | b1157, b1158 | spy0671, spy0655, spy1468 | 529591–570493 | 370.1 |